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> Corrupt sqlite file in repo sl-security?, yum check-update failing
macpheeb
 Posted: Apr 22 2016, 09:44 AM
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I have a Centos 6.2 VM - when I run yum check-update, I get this error -
yum check-update
Loaded plugins: refresh-packagekit, security
sl | 3.5 kB 00:00
sl/primary_db | 4.1 MB 00:04
sl-security | 3.0 kB 00:00
sl-security/primary_db | 15 MB 00:15

Google searches suggest a corrupt sqlite file

od -c /var/cache/yum/x86_64/6.2/sl-security/primary.sqlite | head
0000000 \0 \0 \0 \0 \0 \0 \0 \0 \0 \0 \0 \0 \0 \0 \0 \0
*
0002000 \r \0 \0 \0 \0 004 \0 \0 \0 \0 \0 \0 \0 \0 \0 \0
0002020 \0 \0 \0 \0 \0 \0 \0 \0 \0 \0 \0 \0 \0 \0 \0 \0
*
0014000 \r \0 \0 \0 004 \0 207 \0 \0 207 \0 332 003 002 003 X
0014020 \0 203 \0 \0 \0 \0 \0 \0 \0 \0 \0 \0 \0 \0 \0 \0
0014040 \0 \0 004 201 % 004 \a 027 035 035 001 202 035 t a b
0014060 l e r e q u i r e s r e q u i r
0014100 e s 005 C R E A T E T A B L E


When I compare this to other working sqlite files it seems to lack the header -

0000000 S Q L i t e f o r m a t

Can this be flagged up to the repo maintainers?


Brian
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helikaon
 Posted: Apr 22 2016, 06:06 PM
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Hi Brian,

i think best action you can do is to ask this on the centos mailing list, where surely some centos dev can answer this.

This is a Scientific linux forum and the repositories of SL have nothing to do with Centos repos.


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elisatems
 Posted: Apr 23 2016, 06:23 AM
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QUOTE (helikaon @ Apr 22 2016, 01:06 PM)
Hi Brian,

i think best action you can do is to ask this on the centos mailing list, where surely some centos dev can answer this.

This is a Scientific linux forum and  the repositories of SL have nothing to do with Centos repos.


cheers

I am running Scientific Linux 6.3 and just encountered the same problem today. The offending file is apparently /var/cache/yum/x86_64/6.3/sl-security/primary.sqlite, since running sqlite3 on this file and issuing the .databases command yields the same error (file is encrypted or not a database). Also, as the previous poster stated, the beginning of the file is a series of nulls, very different from the primary.sqlite files in the other repo directories. The other primary.sqlite files seem to contain legitimate databases according to sqlite3.

Doing 'yum clean all' does not fix the problem, since the next time yum is run it recreates the file, and the new file has the same issue.
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macpheeb
 Posted: Apr 23 2016, 10:48 AM
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Sorry - I meant SL 6.2 - I'm juggling RHEL, CentOS and SL here.
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elisatems
 Posted: Apr 24 2016, 01:50 PM
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QUOTE (macpheeb @ Apr 23 2016, 05:48 AM)
Sorry - I meant SL 6.2 - I'm juggling RHEL, CentOS and SL here.

As of this morning yum is working properly again, and /var/cache/yum/x86_64/6.3/sl-security/primary.sqlite contains a valid database again, as confirmed both by sqlite3 and by looking at the file with my text editor. Do you see the same thing?

I'm guessing there was a problem with the repository and the maintainers fixed it.
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macpheeb
 Posted: Apr 24 2016, 05:02 PM
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Thanks for the update my SL 6.2 update checks run fine again.

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